长爪栘[木衣]叶绿体基因组特征系统发育及密码子偏好性分析

Chloroplast genome phylogeny and codon preference of Docynia longiunguis

摘要:

长爪栘[木衣] (Docynia longiunguis Q. Luo & J. L. Liu) 是我国特有的栘[木衣]属植物，具有较高的食药用价值。对其叶绿体基因组进行分析，有助于阐明栘[木衣]属内的系统发育关系，为长爪栘[木衣]资源的开发利用及进一步研究奠定基础。结合其近缘种云南栘[木衣]叶绿体基因组数据，在进行全序列比对后，对其系统发育、密码子偏好性等进行分析。长爪栘[木衣]叶绿体基因组序列总长为158 914 bp (GenBank登录号为MW367027)，总GC含量为36.7%，其中大的单拷贝区(large single-copy, LSC) 长度为87 020 bp，小的单拷贝区(small single-copy, SSC) 长度为19 156 bp，反向重复区(inverted repeats, IRs) 长度为26 369 bp。共注释了102个功能性基因，包括72个蛋白编码基因、26个编码tRNA基因和4个编码rRNA基因。构建系统发育树的最佳模型为TVM+F+R2。系统发育分析结果表明，长爪栘[木衣]与栘[木衣] (Docynia indica (Wall.) Dcne.) 聚为一支，栘[木衣]属物种与苹果属(Malus) 聚为一支。对长爪栘[木衣]及近缘种叶绿体基因组序列进行比对分析，trnY (GUA)-psbD、ndhC-trnV (UAC)、accD-psaI、psbZ-trnFM (CAU) 和ndhF-trnL等区域的变异较大，核酸多样性分析则表明有11处Pi值> 0.01的高变区域，且都位于LSC区及SSC区。除长爪栘[木衣]外，其他序列中均有trnH基因位于IRs/LSC区交界处且都没有越过边界。密码子偏好分析显示，长爪栘[木衣]叶绿体基因中异亮氨酸的密码子编码数量最多，达到了1 205个。长爪栘[木衣]与山荆子(Malus baccata (L.) Borkh.)、三叶海棠(Malus sieboldii (Regel) Rehd.)、湖北海棠(Malus hupehensis (Pamp.) Rehd.) 及木瓜(Chaenomeles sinensis (Thouin) Koehne) 的亲缘关系最近；其叶绿体基因密码子更偏好于使用A/T结尾；长爪栘[木衣]叶绿体基因组与其他蔷薇科植物叶绿体基因组在4个边界区域基因分布显示出较大差异，与同属的云南栘[木衣]及栘[木衣]叶绿体基因组差异相对较小。长爪栘[木衣]叶绿体基因组的组装注释、系统发育分析及序列比对分析，为该物种的资源鉴定、开发和利用提供了理论依据。

Abstract:

Docynia longiunguis is a plant uniquely present in China and is of high edible and medicinal value. The analysis of its chloroplast genome will help clarify the phylogenetic relationship among Docynia and facilitate the development and utilization of D. longiunguis resources. Based on the alignment of chloroplast genome sequences of related species, the phylogeny and codon preference were analyzed. The total length of D. longiunguis chloroplast genome sequence was 158 914 bp (GenBank accession number is MW367027), with an average GC content of 36.7%. The length of the large single-copy (LSC), the small single-copy (SSC), and inverted repeats (IRs) are 87 020 bp, 19 156 bp, and 26 369 bp, respectively. A total of 102 functional genes were annotated, including 72 protein-coding genes, 26 tRNA genes, and 4 rRNA genes. The best model for constructing phylogenetic tree was TVM+F+R2. D. longiunguis and Docynia indica were clustered into a single group, while Docynia and Malus were clustered into a single group. Comparison of the chloroplast genome sequences of D. longiunguis and its five related species revealed that trnY (GUA)-psbD, ndhC-trnV (UAC), accD-psaI, psbZ-trnfM (CAU), ndhF-trnL gene regions varied greatly. The nucleic acid diversity analysis showed that there were 11 high variation areas with nucleotide variability > 0.01, all were located in the LSC and SSC regions. Except for D. longiunguis, the trnH genes in other sequences were located at the IRs/LSC junction and did not cross the boundary. Codon preference analysis showed that D. longiunguis chloroplast genome has the largest number of isoleucine (Ile) codons, up to 1 205. D. longiunguis has the closest genetic relationship with Malus baccata, Malus sieboldii, Malus hupehensis and Chaenomeles sinensis. Its chloroplast genome codon prefers to end with A/T. The chloroplast genome of D. longiunguis and other Rosaceae chloroplast genomes showed great differences in gene distribution in four boundary regions, while relatively small differences from the chloroplast genomes of Docynia delavayi and D. indica of the same genus were observed. The genome annotation, phylogenetic analysis and sequence alignment of chloroplast genome of D. longiunguis may facilitate the identification, development and utilization of this species.